Classify-raster-data

Declare libraries

library(raster)

## Loading required package: sp

library(rhdf5)
library(rgdal)

## rgdal: version: 1.1-10, (SVN revision 622)
##  Geospatial Data Abstraction Library extensions to R successfully loaded
##  Loaded GDAL runtime: GDAL 1.11.4, released 2016/01/25
##  Path to GDAL shared files: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rgdal/gdal
##  Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
##  Path to PROJ.4 shared files: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rgdal/proj
##  Linking to sp version: 1.2-3

Import Canopy Height Model

chm<- raster("../NEONdata/D17-California/TEAK/2013/lidar/TEAK_lidarCHM.tif")
plot(chm, main=" this plots using the raster package")

image(chm, main= "these are just pixels and will stretch the space")

Deal with 0 values

old.hist<-hist(chm)

## Warning in .hist1(x, maxpixels = maxpixels, main = main, plot = plot, ...):
## 32% of the raster cells were used. 100000 values used.

plot(old.hist)

chm[chm==0]<- NA
hist(chm, xlab= "Tree Height (m)")

Import aspect data

aspect<- raster("../NEONdata/D17-California/TEAK/2013//lidar//TEAK_lidarAspect.tif")

plot(aspect, main= "Aspect data for Teakette Field Site")

Create Classification Matrix

#create string of values
# by creating a matrix
class.m<- c(0, 45, 1,
            45, 135, NA,
            135, 225, 2,
            225, 315, NA,
            315, 360, 1)

rcl.m<- matrix(class.m, 
         ncol=3, 
         byrow=TRUE)

rcl.m

##      [,1] [,2] [,3]
## [1,]    0   45    1
## [2,]   45  135   NA
## [3,]  135  225    2
## [4,]  225  315   NA
## [5,]  315  360    1

reclassify raster

asp.ns <- reclassify(aspect, rcl.m)

plot(asp.ns,
     main= "North and South Facing Slopes")

Export Geotiff

writeRaster(asp.ns,
            file="../NEONdata//D17-California//outputs//TEAK/Teak_nsAspect2.tif",
            options= "COMPRESS= LZW",
            NAflag= -9999)

Mask Data

asp.ns

## class       : RasterLayer 
## dimensions  : 577, 543, 313311  (nrow, ncol, ncell)
## resolution  : 1, 1  (x, y)
## extent      : 325963, 326506, 4102905, 4103482  (xmin, xmax, ymin, ymax)
## coord. ref. : +proj=utm +zone=11 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0 
## data source : in memory
## names       : layer 
## values      : 0, 2  (min, max)

ndvi<- raster("../NEONdata//D17-California//TEAK//2013//spectrometer//veg_index//TEAK_NDVI.tif")

plot(ndvi, 
     main= "NDVI for Teakettle Field Site")

#mask data

nFacing.ndvi<- mask(ndvi, 
                    asp.ns) 
plot(nFacing.ndvi)